If you're having gut issues you need to go on the GAPS diet and take high quality probiotics. Your case sounds serious so you'll probably need to do it for at least 2 years.
Take the basic supplements as well (calcium/magnesium, high dose vitamin C, vitamin E, and cod liver oil). When you're able to, make sure to do some light as well as heavy exercise to get your lymphatic system going and to kick start your mitochondria.
It's also important to do coffee enemas probably every single day for at least the first few months.